hcs_cms_reduced
HCA benchmark mixability mouse
suppressPackageStartupMessages({
library(scater)
library(scran)
library(here)
library(magrittr)
library(purrr)
library(dplyr)
library(data.table)
library(Seurat)
library(harmony)
library(scMerge)
library(kBET)
library(CellMixS)
library(jcolors)
})
rseed <- 1234data_path <- here::here("data")
out_path <- here::here("output")
# Create sce list
protocol_names <- c("10X2x5Kcell250Kreads", "C1HTmedium", "C1HTsmall", "CELseq2", "ddSEQ", "Dropseq", "ICELL8", "inDrop", "QUARTZseq", "SCRBseq", "SMARTseq2")
create_sce <- function(protocol){
data <- data.frame(fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")), row.names = 1)
meta_data <- data.frame(fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")), row.names = 1)
colnames(data) <- rownames(meta_data)
sce <- SingleCellExperiment(
assays = list(counts = as.matrix(data)),
colData = meta_data
)
}
sce_list <- protocol_names %>% map(create_sce)## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 10000 column names but the data has 10001 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 5600 column names but the data has 5601 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 6400 column names but the data has 6401 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 2880 column names but the data has 2881 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 28 column names but the data has 29 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 3998 column names but the data has 3999 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 6000 column names but the data has 6001 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 28 column names but the data has 29 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 3892 column names but the data has 3893 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 2982 column names but the data has 2983 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 3068 column names but the data has 3069 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 28 column names but the data has 29 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 3455 column names but the data has 3456 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 19 column names but the data has 20 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_exp_mat.tsv")):
## Detected 2935 column names but the data has 2936 columns (i.e. invalid
## file). Added 1 extra default column name for the first column which is
## guessed to be row names or an index. Use setnames() afterwards if this
## guess is not correct, or fix the file write command that created the file
## to create a valid file.## Warning in fread(paste0(data_path, "/", protocol, "_mouse_metada.tsv")):
## Detected 15 column names but the data has 16 columns (i.e. invalid file).
## Added 1 extra default column name for the first column which is guessed to
## be row names or an index. Use setnames() afterwards if this guess is not
## correct, or fix the file write command that created the file to create a
## valid file.Preprocessing
Filtering and Normalization
#filter
filter_norm <- function(sce){
keep_total_counts <- !isOutlier(sce$total_counts, nmads = 2.5,
type = "both", log = TRUE)
keep_total_features <- !isOutlier(sce$total_features_by_counts, nmads=2.5,
type="both", log=TRUE)
#how to find mito genes?
sce <- sce[, keep_total_counts & keep_total_features]
#create seurat
seurat <- CreateSeuratObject( counts=counts(sce),
meta.data=as.data.frame(colData(sce)),
project = "protocols" )
seurat <- NormalizeData(seurat, verbose = F)
seurat <- FindVariableFeatures(seurat, selection.method = "vst", nfeatures = 10000)
seurat <- ScaleData(seurat)
seurat <- RunPCA(seurat, features = VariableFeatures(object = seurat), verbose = FALSE,
seed.use = rseed, npcs = 10)
seurat <- FindNeighbors(seurat, dims = 1:8)
seurat <- FindClusters(seurat, resolution = 0.6)
seurat <- RunTSNE(seurat, reduction = "pca", dims = 1:8, do.fast = TRUE,
check_duplicates = FALSE, seed.use = rseed )
sce <- SingleCellExperiment(
assays=list(
counts=seurat@assays$RNA@counts,
logcounts=seurat@assays$RNA@data
),
colData=seurat@meta.data,
reducedDims=lapply(seurat@reductions, FUN=function(x) x@cell.embeddings)
)
metadata(sce)$hvg_genes <- seurat@assays$RNA@var.features
sce
}
#sce_list <- lapply(sce_list, filter_norm)
#save
#saveRDS(sce_list, file = paste0(out_path, "/protocol_processed_sce_list_red.rds"))Integrate data
- Combine data
sce_list <- readRDS(file = paste0(out_path, "/protocol_processed_sce_list_red.rds"))
names(sce_list) <- protocol_names
overlap_genes <- Reduce(intersect, map(sce_list, rownames))
overlap_hvg <- Reduce(intersect, map(sce_list, function(x) hvg <- metadata(x)$hvg_genes))
#combine naive
#Mixology dataset
colData(sce_list[[1]])$protocol <- rep(names(sce_list)[1], ncol(sce_list[[1]]))
sce_naive <- sce_list[[1]]
for(i in 2:length(sce_list)){
colData(sce_list[[i]])$protocol <- rep(names(sce_list)[i], ncol(sce_list[[i]]))
coldata_overlap <- intersect(names(colData(sce_naive)), names(colData(sce_list[[i]])))
sce_list[[i]] <- sce_list[[i]][overlap_genes,]
colData(sce_list[[i]]) <- colData(sce_list[[i]])[, coldata_overlap]
colData(sce_naive) <- colData(sce_naive)[, coldata_overlap]
sce_naive <- sce_naive[overlap_genes,]
sce_naive <- cbind(sce_naive, sce_list[[i]])
}
sce_naive <- runPCA(sce_naive, ncomponents = 10)
sce_naive <- runTSNE(sce_naive)
sce_naive <- runUMAP(sce_naive)
#saveRDS(sce_naive, file = paste0(out_path, "/protocol_mouse_reddim_combined_red.rds"))- Integrate data with harmony and scmerge
#load saved res
sce_list <- readRDS(file = paste0(out_path, "/protocol_processed_sce_list_red.rds"))
names(sce_list) <- protocol_names
#sce_naive <- readRDS(file = paste0(out_path, "/protocol_mouse_reddim_combined_red.rds"))
#run harmony
#harmony <- HarmonyMatrix(logcounts(sce_naive), colData(sce_naive), "protocol")
#reducedDims(sce_naive)$harmony <- harmony
#run scMerge
#sce_scmerge <- sce_naive
#data("segList_ensemblGeneID", package = "scMerge") #load reference list mouse
#sce_scmerge$batch <- sce_scmerge$protocol
#assays(sce_scmerge)$logcounts <- as.matrix(assays(sce_scmerge)$logcounts)
#assays(sce_scmerge)$counts <- as.matrix(assays(sce_scmerge)$counts)
#celltype_vec <- sce_list %>% map(function(x){
# n_ct <- length(levels(as.factor(x$seurat_clusters)))}) %>% unlist()
#rownames(sce_scmerge) <-gsub("\\.[0-9]*", "", rownames(sce_scmerge))
#sce_scMerge <- scMerge(
# sce_combine = sce_scmerge,
# ctl = segList_ensemblGeneID$mouse$mouse_scSEG,
# kmeansK = celltype_vec,
# assay_name = "scmerge",
# fast_svd = TRUE,
# rsvd_prop = 0.1)
#saveRDS(sce_naive, file = paste0(out_path, "/integrated_protocols_mouse_red.rds"))
sce_naive <- readRDS(file = paste0(out_path, "/integrated_protocols_mouse_red.rds"))Plot combined data
plotReducedDim(sce_naive, use_dimred = "PCA",
colour_by = "protocol") +
ggtitle("No batch correction")
plotReducedDim(sce_naive, use_dimred = "UMAP",
colour_by = "protocol") +
ggtitle("No batch correction")
plotReducedDim(sce_naive, use_dimred = "harmony",
colour_by = "protocol") +
ggtitle("harmony")
#plotReducedDim(sce_naive, use_dimred = "pca_scmerge",
# colour_by = "protocol") +
# ggtitle("scmerge")
#plotReducedDim(sce_naive, use_dimred = "umap_scmerge",
# colour_by = "protocol") +
# ggtitle("scmerge")Evaluate mixing
## cms all
sce_naive$protocol <- as.factor(sce_naive$protocol)
sce_naive <- cms(sce_naive, k = 300, group = "protocol", dim_red = "PCA", res_name = "naive", cell_min = 30, n_dim = 10)## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculationsce_naive <- cms(sce_naive, k = 300, group = "protocol", dim_red = "harmony", res_name = "harmony", cell_min = 30)## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculationsce_naive <- ldfDiff(sce_pre_list = sce_list, sce_combined = sce_naive, group = "protocol", k = 300, dim_combined = "harmony", res_name = "harmony")## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in .defineSubspace(sce_pre, assay_pre, dim_red, n_dim): 'dim_red' not found:
## PCA subspace is used to calculate distances.## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculationsaveRDS(sce_naive, file = paste0(out_path, "/cms_all_mouse_red.rds"))Plot cms all
#sce_naive <- readRDS(file = paste0(out_path, "/cms_all_mouse_red.rds"))
#naive
visHist(sce_naive, n_col = 2)
visGroup(sce_naive, "protocol", dim_red = "UMAP")
visMetric(sce_naive, metric_var = "cms_smooth.naive", dim_red = "UMAP")
visCluster(sce_naive, cluster_var = "protocol", metric_var = "cms_smooth.naive")## Picking joint bandwidth of 0.00609
#harmony
visGroup(sce_naive, "protocol", dim_red = "harmony")
visMetric(sce_naive, metric_var = "cms_smooth.harmony", dim_red = "harmony")
visCluster(sce_naive, cluster_var = "protocol", metric_var = "cms_smooth.harmony")## Picking joint bandwidth of 0.0141
visIntegration(sce_naive, metric_prefix = "cms_smooth")## Picking joint bandwidth of 0.00766
visMetric(sce_naive, metric_var = "diff_ldf.harmony", dim_red = "harmony")
visCluster(sce_naive, cluster_var = "protocol", metric_var = "diff_ldf.harmony")## Picking joint bandwidth of 0.0831
Summarize scores
col_group <-c(c(jcolors('pal6'), jcolors('pal8'))[c(1,8,14,5,2:4,6,7)], rev(jcolors('pal4')))
names(col_group) <- c()
mean_tab <- as_tibble(colData(sce_naive)) %>% dplyr::group_by(protocol) %>% summarize("naive_cms" = mean(cms_smooth.naive), "ldf_mean" = mean(abs(diff_ldf.harmony)), "harmony_cms" = mean(cms.harmony))
ggplot(mean_tab, aes(x= ldf_mean, y = harmony_cms, colour = protocol)) +
geom_point(size = 4.5) +
scale_color_manual(values = col_group) +
theme_bw()
ggplot(mean_tab, aes(x= naive_cms, y = harmony_cms, colour = protocol)) +
geom_point(size = 4.5) +
scale_color_manual(values = col_group) +
theme_bw()
Compare protocolwise
cms_split_protocol <- function(protocol1){
protocol2_list <- protocol_names[-which(protocol_names %in% protocol1)]
sce_split_list <- lapply(protocol2_list, function(protocol2){
sce_split <- sce_naive[,sce_naive$protocol %in% c(protocol1, protocol2)]
sce_split <- cms(sce_split, k = 200, group = "protocol", dim_red = "PCA",
res_name = paste0("naive_", protocol1, "_", protocol2), cell_min = 30, n_dim = 10)
sce_split <- cms(sce_split, k = 200, group = "protocol", dim_red = "harmony",
res_name = paste0("harmony_", protocol1, "_", protocol2), cell_min = 30)
sce_split
})
names(sce_split_list) <- protocol2_list
return(sce_split_list)
}
cms_split_list <- lapply(protocol_names, cms_split_protocol)## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
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## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculation## Warning in (function (jobs, data, centers, info, distance, k, get.index, :
## tied distances detected in nearest-neighbor calculationnames(cms_split_list) <- protocol_names
saveRDS(sce_naive, file = paste0(out_path, "/cms_split_list.rds"))